@article{14831, abstract = {Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis.}, author = {Sakref, Yann and Muñoz Basagoiti, Maitane and Zeravcic, Zorana and Rivoire, Olivier}, issn = {1520-5207}, journal = {The Journal of Physical Chemistry B}, keywords = {Materials Chemistry, Surfaces, Coatings and Films, Physical and Theoretical Chemistry}, number = {51}, pages = {10950--10959}, publisher = {American Chemical Society}, title = {{On kinetic constraints that catalysis imposes on elementary processes}}, doi = {10.1021/acs.jpcb.3c04627}, volume = {127}, year = {2023}, } @article{11340, abstract = {Like-charge attraction, driven by ionic correlations, challenges our understanding of electrostatics both in soft and hard matter. For two charged planar surfaces confining counterions and water, we prove that, even at relatively low correlation strength, the relevant physics is the ground-state one, oblivious of fluctuations. Based on this, we derive a simple and accurate interaction pressure that fulfills known exact requirements and can be used as an effective potential. We test this equation against implicit-solvent Monte Carlo simulations and against explicit-solvent simulations of cement and several types of clays. We argue that water destructuring under nanometric confinement drastically reduces dielectric screening, enhancing ionic correlations. Our equation of state at reduced permittivity therefore explains the exotic attractive regime reported for these materials, even in the absence of multivalent counterions.}, author = {Palaia, Ivan and Goyal, Abhay and Del Gado, Emanuela and Šamaj, Ladislav and Trizac, Emmanuel}, issn = {1520-5207}, journal = {Journal of Physical Chemistry B}, number = {16}, pages = {3143--3149}, publisher = {American Chemical Society}, title = {{Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring}}, doi = {10.1021/acs.jpcb.2c00028}, volume = {126}, year = {2022}, } @article{10357, abstract = {The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.}, author = {Dear, Alexander J. and Šarić, Anđela and Michaels, Thomas C. T. and Dobson, Christopher M. and Knowles, Tuomas P. J.}, issn = {1520-5207}, journal = {The Journal of Physical Chemistry B}, keywords = {materials chemistry}, number = {49}, pages = {11721--11730}, publisher = {American Chemical Society}, title = {{Statistical mechanics of globular oligomer formation by protein molecules}}, doi = {10.1021/acs.jpcb.8b07805}, volume = {122}, year = {2018}, } @article{8453, abstract = {Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns–ms) time scales. The measurement of heteronuclear (13C, 15N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1ρ relaxation) provides access to such motions, and an increasing number of studies involving R1ρ relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that the CCR rate constant depends on ns–ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1ρ rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation.}, author = {Kurauskas, Vilius and Weber, Emmanuelle and Hessel, Audrey and Ayala, Isabel and Marion, Dominique and Schanda, Paul}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, keywords = {Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films}, number = {34}, pages = {8905--8913}, publisher = {American Chemical Society}, title = {{Cross-correlated relaxation of dipolar coupling and chemical-shift anisotropy in magic-angle spinning R1ρ NMR measurements: Application to protein backbone dynamics measurements}}, doi = {10.1021/acs.jpcb.6b06129}, volume = {120}, year = {2016}, } @article{10390, abstract = {We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases, which includes most of the mesophases observed in self-assembly of block copolymers but also crystalline structures formed by asymmetric, hard binary mixtures. Our results detail the phenomenological behavior of these systems when softness is introduced in terms of two different classes of interparticle interactions: (a) the elastic Hertz potential, which has a finite energy cost for complete overlap of any two components, and (b) a generic power-law repulsion with tunable exponent. We discuss how simple geometric arguments can be used to account for the large structural variety observed in these systems and detail the similarities and differences in the phase behavior for the two classes of potentials under consideration.}, author = {Šarić, Anđela and Bozorgui, Behnaz and Cacciuto, Angelo}, issn = {1520-5207}, journal = {The Journal of Physical Chemistry B}, keywords = {materials chemistry}, number = {22}, pages = {7182--7189}, publisher = {American Chemical Society}, title = {{Packing of soft asymmetric dumbbells}}, doi = {10.1021/jp107545w}, volume = {115}, year = {2010}, } @article{7780, abstract = {We used single-channel electrical recordings and Langevin molecular dynamics simulations to explore the electrophoretic translocation of various β-hairpin peptides across the staphylococcal α-hemolysin (αHL) protein pore at single-molecule resolution. The β-hairpin peptides, which varied in their folding properties, corresponded to the C terminal residues of the B1 domain of protein G. The translocation time was strongly dependent on the electric force and was correlated with the folding features of the β-hairpin peptides. Highly unfolded peptides entered the pore in an extended conformation, resulting in fast single-file translocation events. In contrast, the translocation of the folded β-hairpin peptides occurred more slowly. In this case, the β-hairpin peptides traversed the αHL pore in a misfolded or fully folded conformation. This study demonstrates that the interaction between a polypeptide and a β-barrel protein pore is dependent on the folding features of the polypeptide. }, author = {Goodrich, Carl Peter and Kirmizialtin, Serdal and Huyghues-Despointes, Beatrice M. and Zhu, Aiping and Scholtz, J. Martin and Makarov, Dmitrii E. and Movileanu, Liviu}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, number = {13}, pages = {3332--3335}, publisher = {American Chemical Society}, title = {{Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations}}, doi = {10.1021/jp071364h}, volume = {111}, year = {2007}, } @article{13430, abstract = {Dynamic self-assembly (DySA) processes occurring outside of thermodynamic equilibrium underlie many forms of adaptive and intellligent behaviors in natural systems. Relatively little, however, is known about the principles that govern DySA and the ways in which it can be extended to artificial ensembles. This article discusses recent advances in both the theory and the practice of nonequilibrium self-assembly. It is argued that a union of ideas from thermodynamics and dynamic systems' theory can provide a general description of DySA. In parallel, heuristic design rules can be used to construct DySA systems of increasing complexities based on a variety of suitable interactions/potentials on length scales from nanoscopic to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also discussed.}, author = {Fialkowski, Marcin and Bishop, Kyle J. M. and Klajn, Rafal and Smoukov, Stoyan K. and Campbell, Christopher J. and Grzybowski, Bartosz A.}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, keywords = {Materials Chemistry, Surfaces, Coatings and Films, Physical and Theoretical Chemistry}, number = {6}, pages = {2482--2496}, publisher = {American Chemical Society}, title = {{Principles and implementations of dissipative (dynamic) self-assembly}}, doi = {10.1021/jp054153q}, volume = {110}, year = {2006}, }